This seems to be a bug in Filemaker as the layout is not displaying correctly in Webdirect. If there's a corruption in the Theme then repairing the file should fix it - hence why I think it's a bug.
I have attached an image of how it displays in Filemaker, Webdirect 14 and also the file.
The only way I can think of to fix it is to rebuild the entire theme, but this is a massive pain. Any other suggestions?